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7 Uses of Class compbio.engine.client.CommandBuilder
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18 parent.document.title="Uses of Class compbio.engine.client.CommandBuilder";
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42 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
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84 <B>Uses of Class<br>compbio.engine.client.CommandBuilder</B></H2>
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87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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88 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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90 Packages that use <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>
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92 <TR BGCOLOR="white" CLASS="TableRowColor">
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93 <TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>
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94 <TD> </TD>
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96 <TR BGCOLOR="white" CLASS="TableRowColor">
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97 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>
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98 <TD>Utilities commonly used by all runners. </TD>
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100 <TR BGCOLOR="white" CLASS="TableRowColor">
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101 <TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>
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102 <TD> </TD>
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104 <TR BGCOLOR="white" CLASS="TableRowColor">
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105 <TD><A HREF="#compbio.runner.conservation"><B>compbio.runner.conservation</B></A></TD>
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106 <TD> </TD>
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108 <TR BGCOLOR="white" CLASS="TableRowColor">
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109 <TD><A HREF="#compbio.runner.disorder"><B>compbio.runner.disorder</B></A></TD>
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110 <TD> </TD>
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112 <TR BGCOLOR="white" CLASS="TableRowColor">
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113 <TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>
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114 <TD>Wrappers for native executables for multiple sequence alignment (msa) </TD>
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119 <A NAME="compbio.engine.client"><!-- --></A>
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120 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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121 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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122 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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123 Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>
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129 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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130 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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131 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>
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133 <TR BGCOLOR="white" CLASS="TableRowColor">
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134 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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135 <CODE> <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><?></CODE></FONT></TD>
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136 <TD><CODE><B>RunConfiguration.</B><B><A HREF="../../../../compbio/engine/client/RunConfiguration.html#getParameters()">getParameters</A></B>()</CODE>
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139 </TD>
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141 <TR BGCOLOR="white" CLASS="TableRowColor">
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142 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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143 <CODE> <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="type parameter in ConfiguredExecutable">T</A>></CODE></FONT></TD>
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144 <TD><CODE><B>ConfiguredExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html#getParameters()">getParameters</A></B>()</CODE>
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147 </TD>
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149 <TR BGCOLOR="white" CLASS="TableRowColor">
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150 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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151 <CODE> <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></FONT></TD>
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152 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getParameters()">getParameters</A></B>()</CODE>
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155 </TD>
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157 <TR BGCOLOR="white" CLASS="TableRowColor">
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158 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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159 <CODE> <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>></CODE></FONT></TD>
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160 <TD><CODE><B>Executable.</B><B><A HREF="../../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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163 </TD>
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165 <TR BGCOLOR="white" CLASS="TableRowColor">
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166 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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167 <CODE> <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>
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168 <TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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171 </TD>
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173 <TR BGCOLOR="white" CLASS="TableRowColor">
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174 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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175 <CODE> <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></FONT></TD>
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176 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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179 </TD>
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181 <TR BGCOLOR="white" CLASS="TableRowColor">
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182 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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184 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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185 <TR ALIGN="right" VALIGN="">
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186 <TD NOWRAP><FONT SIZE="-1">
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187 <CODE><T> <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><T></CODE></FONT></TD>
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190 </CODE></FONT></TD>
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191 <TD><CODE><B>CommandBuilder.</B><B><A HREF="../../../../compbio/engine/client/CommandBuilder.html#newCommandBuilder(java.util.List, java.lang.String)">newCommandBuilder</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><? extends <A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><T>> arguments,
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192 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> nameValueSeparator)</CODE>
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195 This produces the same result as getCommands method.</TD>
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201 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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202 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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203 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with parameters of type <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>
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205 <TR BGCOLOR="white" CLASS="TableRowColor">
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206 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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207 <CODE> void</CODE></FONT></TD>
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208 <TD><CODE><B>RunConfiguration.</B><B><A HREF="../../../../compbio/engine/client/RunConfiguration.html#setParameters(compbio.engine.client.CommandBuilder)">setParameters</A></B>(<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><?> parameters)</CODE>
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211 </TD>
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216 <A NAME="compbio.runner"><!-- --></A>
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217 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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218 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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219 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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220 Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A> in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>
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226 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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227 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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228 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> that return <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>
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230 <TR BGCOLOR="white" CLASS="TableRowColor">
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231 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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232 <CODE> <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></CODE></FONT></TD>
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233 <TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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236 <B>Deprecated.</B> </TD>
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241 <A NAME="compbio.runner._impl"><!-- --></A>
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242 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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243 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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244 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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245 Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A> in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>
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251 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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252 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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253 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that return <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>
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255 <TR BGCOLOR="white" CLASS="TableRowColor">
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256 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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257 <CODE> <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>></CODE></FONT></TD>
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258 <TD><CODE><B>NetNglyc.</B><B><A HREF="../../../../compbio/runner/_impl/NetNglyc.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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261 </TD>
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266 <A NAME="compbio.runner.conservation"><!-- --></A>
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267 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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268 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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269 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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270 Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A> in <A HREF="../../../../compbio/runner/conservation/package-summary.html">compbio.runner.conservation</A></FONT></TH>
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276 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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277 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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278 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/conservation/package-summary.html">compbio.runner.conservation</A> that return <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>
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280 <TR BGCOLOR="white" CLASS="TableRowColor">
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281 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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282 <CODE> <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>></CODE></FONT></TD>
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283 <TD><CODE><B>AACon.</B><B><A HREF="../../../../compbio/runner/conservation/AACon.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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286 </TD>
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291 <A NAME="compbio.runner.disorder"><!-- --></A>
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292 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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293 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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294 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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295 Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A> in <A HREF="../../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A></FONT></TH>
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301 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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302 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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303 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A> that return <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>
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305 <TR BGCOLOR="white" CLASS="TableRowColor">
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306 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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307 <CODE> <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>></CODE></FONT></TD>
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308 <TD><CODE><B>Jronn.</B><B><A HREF="../../../../compbio/runner/disorder/Jronn.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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311 </TD>
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316 <A NAME="compbio.runner.msa"><!-- --></A>
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317 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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318 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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319 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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320 Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>
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326 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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327 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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328 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>
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330 <TR BGCOLOR="white" CLASS="TableRowColor">
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331 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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332 <CODE> <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>></CODE></FONT></TD>
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333 <TD><CODE><B>Tcoffee.</B><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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336 </TD>
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338 <TR BGCOLOR="white" CLASS="TableRowColor">
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339 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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340 <CODE> <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>></CODE></FONT></TD>
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341 <TD><CODE><B>ClustalO.</B><B><A HREF="../../../../compbio/runner/msa/ClustalO.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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344 </TD>
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352 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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353 <A NAME="navbar_bottom"><!-- --></A>
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354 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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355 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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358 <A NAME="navbar_bottom_firstrow"><!-- --></A>
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359 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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360 <TR ALIGN="center" VALIGN="top">
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361 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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362 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
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363 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
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364 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
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365 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
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366 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
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367 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
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368 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
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372 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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378 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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380 NEXT</FONT></TD>
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381 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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382 <A HREF="../../../../index.html?compbio/engine/client/\class-useCommandBuilder.html" target="_top"><B>FRAMES</B></A>
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383 <A HREF="CommandBuilder.html" target="_top"><B>NO FRAMES</B></A>
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384 <SCRIPT type="text/javascript">
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387 document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
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392 <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
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